| Shakespeare & CompanyEIN 04-2666826 | Arts, Culture, Humanities | MA | $4,795,855Mid-sized | 82.41 |
| Shakespeare Theatre CompanyEIN 52-1405988 | Arts, Culture, Humanities | DC | $21,930,518Large | 87.67 |
| Shalom AustinEIN 74-1469465 | Human Services | TX | $13,606,228Large | 85.00 |
| Shalom FoundationEIN 95-4894733 | International | TN | $830,312Small | 85.00 |
| Shane's InspirationEIN 95-4760497 | Human Services | CA | $2,205,495Small | 83.43 |
| ShantiEIN 94-2297147 | Health | CA | $4,966,512Mid-sized | 86.47 |
| Share Our StrengthEIN 52-1367538 | Human Services | DC | $51,056,766Large | 80.07 |
| Shared Harvest FoodbankEIN 31-1096571 | Human Services | OH | $9,251,021Mid-sized | 86.64 |
| Shared InterestEIN 13-3836581 | International | NY | $2,086,363Small | 89.75 |
| Sharing HouseEIN 56-1292875 | Human Services | NC | $1,429,960Small | 89.52 |
| Shelburne Museum EIN 03-0179436 | Arts, Culture, Humanities | VT | $6,774,923Mid-sized | 84.15 |
| Shelby Humane SocietyEIN 63-0817987 | Animals | AL | $1,471,576Small | 88.41 |
| Sheltering Arms Early Education & Family CentersEIN 58-0566236 | Education | GA | $30,964,764Large | 89.87 |
| Shelterwood EIN 23-7362463 | Religion | MO | $5,554,488Mid-sized | 88.96 |
| Shepherd's GateEIN 94-2902803 | Human Services | CA | $5,006,170Mid-sized | 88.98 |
| Shepherd's TableEIN 52-1381738 | Human Services | MD | $1,756,776Small | 87.77 |
| Sheriff's Youth Foundation of Los Angeles CountyEIN 95-4047797 | Human Services | CA | $1,407,444Small | 87.30 |
| Shiloh Christian Children's RanchEIN 43-1122941 | Human Services | MO | $1,982,671Small | 86.85 |
| SHRM FoundationEIN 34-6610067 | Education | VA | $2,302,725Small | 86.65 |
| SIECUSEIN 13-2508249 | Health | DC | $501,716Small | 86.71 |
| SIFATEIN 63-0776048 | Religion | AL | $1,873,811Small | 82.62 |
| Sight ConnectionEIN 91-0564751 | Health | WA | $1,299,791Small | 86.27 |
| Silicon Valley CreatesEIN 94-2825213 | Arts, Culture, Humanities | CA | $2,479,545Small | 88.98 |
| Silicon Valley Education FoundationEIN 20-5061316 | Education | CA | $5,764,125Mid-sized | 86.21 |
| SilkroadEIN 04-3444069 | Arts, Culture, Humanities | MA | $4,595,602Mid-sized | 87.29 |
| Siloam Family Health CenterEIN 58-1867940 | Health | TN | $3,783,730Mid-sized | 88.66 |
| Simon Youth FoundationEIN 35-2035269 | Education | IN | $3,755,110Mid-sized | 88.63 |
| Single Stop USAEIN 20-8837690 | Human Services | NY | $21,924,829Large | 80.68 |
| Sioux Falls Area Humane SocietyEIN 46-0239786 | Animals | SD | $1,675,972Small | 80.82 |
| Sitar Arts CenterEIN 52-2113471 | Human Services | DC | $1,914,367Small | 88.36 |
| SITE Santa FeEIN 85-0413922 | Arts, Culture, Humanities | NM | $2,574,910Small | 88.61 |
| Sjögren's Syndrome FoundationEIN 11-2779073 | Health | MD | $2,169,805Small | 84.78 |
| Skid Row Housing TrustEIN 95-4205316 | Community Development | CA | $21,003,687Large | 81.70 |
| Skirball Cultural CenterEIN 95-4538371 | Arts, Culture, Humanities | CA | $25,294,003Large | 87.83 |
| SMARTEIN 93-1051724 | Education | OR | $3,497,122Small | 87.37 |
| Smith Center for Healing and the ArtsEIN 52-1977976 | Health | DC | $1,357,229Small | 89.35 |
| Smoky Mountain Children's HomeEIN 23-7110635 | Human Services | TN | $8,664,116Mid-sized | 87.30 |
| Smuin BalletEIN 94-3197247 | Arts, Culture, Humanities | CA | $4,135,237Mid-sized | 88.33 |
| Social Venture PartnersEIN 91-1894424 | Research and Public Policy | WA | $2,722,955Small | 83.35 |
| Society for Women's Health ResearchEIN 52-1694732 | Human and Civil Rights | DC | $1,749,602Small | 81.80 |
| Society of St. Vincent de Paul ChicagoEIN 36-3195567 | Human Services | IL | $4,872,627Mid-sized | 82.73 |
| Society of St. Vincent de Paul of Alameda CountyEIN 94-1156493 | Human Services | CA | $5,959,918Mid-sized | 84.57 |
| Society of St. Vincent de Paul of San Mateo CountyEIN 94-1375833 | Human Services | CA | $6,229,067Mid-sized | 87.77 |
| Society of St. Vincent de Paul, Portland CouncilEIN 93-0456525 | Human Services | OR | $7,058,723Mid-sized | 86.84 |
| Society of the CincinnatiEIN 53-0205423 | Arts, Culture, Humanities | DC | $4,196,909Mid-sized | 88.52 |
| Society of the Four ArtsEIN 59-0454318 | Arts, Culture, Humanities | FL | $8,133,941Mid-sized | 86.63 |
| Sojourner Family Peace CenterEIN 39-1276210 | Human Services | WI | $7,587,653Mid-sized | 83.73 |
| SojournersEIN 23-7380554 | Religion | DC | $5,042,915Mid-sized | 81.65 |
| Solar Electric Light FundEIN 52-1701564 | International | DC | $4,497,399Mid-sized | 89.02 |
| Solve ME/CFS InitiativeEIN 56-1683450 | Health | CA | $1,925,767Small | 88.69 |
| Sonoma Valley Education FoundationEIN 68-0279152 | Education | CA | $1,722,094Small | 81.79 |
| Sonoran InstituteEIN 86-0684610 | Environment | AZ | $2,969,310Small | 82.94 |
| SOS International/SOS LocalEIN 87-0657642 | International | TX | $7,449,709Mid-sized | 88.68 |
| South Boston Neighborhood HouseEIN 04-2104807 | Human Services | MA | $1,756,067Small | 84.90 |
| South Carolina Governor's School for Science and Math FoundationEIN 57-0881347 | Education | SC | $2,340,649Small | 86.43 |
| South Coast RepertoryEIN 95-6122708 | Arts, Culture, Humanities | CA | $11,651,004Mid-sized | 86.11 |
| South Coastal Counties Legal Services, Inc.EIN 04-3330208 | Human and Civil Rights | MA | $5,224,199Mid-sized | 87.14 |
| South Dakota Symphony OrchestraEIN 46-6017026 | Arts, Culture, Humanities | SD | $1,927,737Small | 83.34 |
| South Florida MuseumEIN 59-0598726 | Arts, Culture, Humanities | FL | $3,401,335Small | 87.76 |
| South Hills Interfaith MovementEIN 25-1213332 | Human Services | PA | $2,330,337Small | 88.07 |